Related papers: A Minimal OO Calculus for Modelling Biological Sys…
We propose a novel proof technique that can be applied to attack a broad class of problems in computational complexity, when switching the order of universal and existential quantifiers is helpful. Our approach combines the standard min-max…
A prominent approach to implementing ontology-mediated queries (OMQs) is to rewrite into a first-order query, which is then executed using a conventional SQL database system. We consider the case where the ontology is formulated in the…
We present the novel approach to mathematical modeling of information processes in biosystems. It explores the mathematical formalism and methodology of quantum theory, especially quantum measurement theory. This approach is known as {\it…
The statements `inheritance is not subtyping' and `mainstream OO languages unnecessarily place restrictions over inheritance' have rippled as mantras through the PL research community for years. Many mainstream OO developers and OO language…
The depth-bounded fragment of the pi-calculus is an expressive class of systems enjoying decidability of some important verification problems. Unfortunately membership of the fragment is undecidable. We propose a novel type system,…
Design patterns are distilled from many real systems to catalog common programming practice. However, some object-oriented design patterns are distorted or overly complicated because of the lack of supporting programming language constructs…
The univalence axiom expresses the principle of extensionality for dependent type theory. However, if we simply add the univalence axiom to type theory, then we lose the property of canonicity - that every closed term computes to a…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
In this paper, we propose the use of a modeling methodology based on the notion of thing, with a focus on the current stage of research being on the analysis phase of software system modeling. The object-oriented approach, which takes the…
Cell injection is an approach used for the delivery of small sample substances into a biological cell and is widely used in drug development, gene injection, intracytoplasmic sperm injection (ICSI) and in-virto fertilization (IVF). Robotic…
This paper presents a grammar formalism designed for use in data-oriented approaches to language processing. The formalism is best described as a right-linear indexed grammar extended in linguistically interesting ways. The paper goes on to…
An invitation to simulation is made into a realizable challenge: the reader is taken from scratch to games with words, to mathematical models, to statistical analysis, to simulation of evolution. No special requirements are needed: we work…
We investigate a technique from the literature, called the phantom-types technique, that uses parametric polymorphism, type constraints, and unification of polymorphic types to model a subtyping hierarchy. Hindley-Milner type systems, such…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
We prove that orthogonal constructor term rewrite systems and lambda-calculus with weak (i.e., no reduction is allowed under the scope of a lambda-abstraction) call-by-value reduction can simulate each other with a linear overhead. In…
Existential rules are an expressive knowledge representation language mainly developed to query data. In the literature, they are often supposed to be in some normal form that simplifies technical developments. For instance, a common…
Pattern-based, modular ontologies have several beneficial properties that lend themselves to FAIR data practices, especially as it pertains to Interoperability and Reusability. However, developing such ontologies has a high upfront cost,…
The aim of this paper is to propose a strategy to implement the Minimal Model Program in modern computer algebra systems.
We show that when we endow the action principle with the overlooked possibility to allow endpoint selection, it gains an enormous additional power, which, perhaps surprisingly, directly corresponds to biological behavior. The biological…
As widely known, the basic reproduction number plays a key role in weighing birth/infection and death/recovery processes in several models of population dynamics. In this general setting, its characterization as the spectral radius of next…